SAPP produces two sections of output: an HTML page of output tables, and an image (.png) or html file with the resulting phylogenetic tree. The HTML page is printed first and at the bottom you will see a “Get SAPP Tree” button which will download the image (or html) file.
The HTML Page
Program status messages and errors will appear on this page, as well as four output tables:
1) STR Table. This table is included to verify the STR input. It starts with the calculated Group Modal for your input set (if you have included your own Modal in the input data that will be shown instead). This is followed by all the input kits with the off-modals colored.
2) Original Genetic Distance Table. This table calculates genetic distances (GDs) from the input STR results alone. It should match closely (perhaps not exactly) with GD calculations from other tools and commercial companies.
3) Adjusted Genetic Distance Table. This table re-calculates the GDs based on the tree that SAPP has just calculated. It should therefore be a better indicator of the true genetic distance since it will correct for any convergence that may have occurred in the calculated tree. Note that this table will change as SAPP produces new trees for other combinations of STRs and SNPs and genealogies.
4) Kit to SNP/Genealogy Cross-Reference. This table summarizes the input SNP and Genealogy data showing the +. -. or ? status against the various kits. This is included to verify your SNP and Genealogy input, as well as to show what SNP inclusion/exclusion decisions SAPP has made on its own from its knowledge of the Y-SNP haplotree.
The Image or HTML Tree File
This is a downloaded file containing the phylogenetic tree. Normally the tree is drawn as a graphic (PNG image). Kits are shown in yellow boxes; calculated nodes are shown in blue.
Boxes are connected by lines of varying thickness, indicating how confident SAPP is in those connections. There are three “levels” of confidence – thick blue lines based on unambiguous STR, SNP, or Genealogy data; thinner blue lines based on less certain data (often on STR data alone), or thin grey lines where SAPP made what it thought was the best decision among several close choices without clear SNP or Genealogy support.
Within boxes there are three labels – the kit or node number in the middle, TMRCA calculations in green, and SNP and Genealogy labels in blue. SNPs and Genealogy labels are marked on the nodes for the MRCA ancestor for that Genealogy label or from which that SNP descends. In cases where kits are marked “unknown” for that SNP or Genealogy label there may be a range of nodes which are the possible MRCA for that SNP/Genealogy label; in those cases the label is marked as “Label>” on the lowest possible node and “<Label” on the highest possible node. The actual MRCA node for that SNP or ancestor could be at either of those nodes or any of the nodes in between.
The TMRCA information in the boxes represents the average Time to Most Recent Common Ancestor for the subbranches immediately below that box. TMRCA estimates have a fairly wide error range, so the boxes show the most likely estimate first, with the 67% range (one standard deviation) boundaries next in brackets. TMRCAs are shown both in generations and year (BC/AD) formats, using 28 years per generation and rounded to the nearest generation or nearest 50 years.
If you have many kits in your data (say, 200 or more) the tree as an image can become too large for many viewing applications to handle, and certainly too large to print or easily absorb. In that case you can switch to showing the resulting tree in text form as an HTML file (see the TEXTOUT option in the /OPTIONS section under Inputs). Each node or kit is shown on its own line, numbered and indented according to its depth in the tree. The TMRCA and SNP/Genealogy label information is shown next to each node or kit, and STR mutations are shown immediately above.
These are just the major differences in output; SAPP has too many options and optional sections to easily explain all the other information and colors that can be added to the tree. See the Inputs page or the training videos for an explanation of these options and try them out!